Structure of the glucocorticoid receptor (NR3C1) gene 5′ untranslated region: identification, and tissue distribution of multiple new human exon 1

The 5′ untranslated region (UTR) of the glucocorticoid receptor (GR) plays a key role in determining tissue-specific expression and protein isoforms. Analysis of the 5′ UTR of the human GR (hGR) has revealed 11 splice variants of the hGR exon 1, based on seven exon 1s, four of which (1-D to 1-F and 1-H) were previously unknown. All of the exon 1 variants have unique splice donor sites and share a common exon 2 splice acceptor site. Due to an upstream in-frame TGA stop codon the predicted translation from all splice variants is identical. The four new exon 1s show remarkable similarity with their rat homologues. Exon 1-D starts and finishes 17 and 36 bp upstream of the corresponding ends of the rat exon 14. Exon 1-E is only 6 bp longer than its homologue exon 15. Exon 1-F contains two short inserts of 11 and 6 bp when compared with the rat 17. 1-H is 18 bp longer than the corresponding rat 111. In addition to these new exons, we found that the human exon 1-C occurs as three distinct splice variants, covering the region homologous to the rat exons 19 and 110. All of the alternative hGR exons 1s presented here were found to be transcribed in human tissue. The human hippocampus expresses mRNA of all the exon 1 variants, while the expression of the other exon 1s seems to be tissue specific. While exon 1-D is only in the hippocampus, exons 1-E and 1-F are also detected in the immune system, and exon 1-H additionally in the liver, lung and smooth muscle. The 5′ region of the hGR is more complex than previously thought, and we suggest that each of these untranslated first exons have a distinct proximal promoter region, providing additional depth to the mechanisms available for tissue-specific expression of the hGR isoforms.

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Alternative promoter usage and alternative splicing contribute to mRNA heterogeneity of mouse monocarboxylate transporter 2

Physiological Genomics ◽

10.1152/physiolgenomics.00192.2007 ◽

2007 ◽

Vol 32 (1) ◽

pp. 95-104 ◽

Cited By ~ 11

Author(s):

Shelley X. L. Zhang ◽

Tina R. Searcy ◽

Yiman Wu ◽

David Gozal ◽

Yang Wang

Keyword(s):

Transcription Factors ◽

Alternative Splicing ◽

Alternative Promoter ◽

Monocarboxylate Transporter ◽

Specific Expression ◽

Exon 2 ◽

Tissue Specific ◽

Tissue Specific Expression ◽

Exon 1 ◽

Promoter Usage

Expression patterns of monocarboxylate transporter 2 (MCT2) display mRNA diversity in a tissue-specific fashion. We cloned and characterized multiple mct2 5′-cDNA ends from the mouse and determined the structural organization of the mct2 gene. We found that transcription of this gene was initiated from five independent genomic regions that spanned >80 kb on chromosome 10, resulting in five unique exon 1 variants (exons 1a, 1b, 1c, 1d, and 1e) that were then spliced to the common exon 2. Alternative splicing of four internal exons (exons AS1, AS2, AS3, and exon 3) greatly increased the complexity of mRNA diversity. While exon 1c was relatively commonly used for transcription initiation in various tissues, other exon 1 variants were used in a tissue-specific fashion, especially exons 1b and 1d that were used exclusively for testis-specific expression. Sequence analysis of 5′-flanking regions upstream of exons 1a, 1b, and 1c revealed the presence of numerous potential binding sites for ubiquitous transcription factors in all three regions and for transcription factors implicated in testis-specific or hypoxia-induced gene expression in the 1b region. Transient transfection assays demonstrated that each of the three regions contained a functional promoter and that the in vitro, cell type-specific activities of these promoters were consistent with the tissue-specific expression pattern of the mct2 gene in vivo. These results indicate that tissue-specific expression of the mct2 gene is controlled by multiple alternative promoters and that both alternative promoter usage and alternative splicing contribute to the remarkable mRNA diversity of the gene.

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The mouse carbonic anhydrase I gene contains two tissue-specific promoters

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3308-3313.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3308-3313

Author(s):

P Fraser ◽

P Cummings ◽

P Curtis

Keyword(s):

Carbonic Anhydrase ◽

Splice Acceptor Site ◽

Acceptor Site ◽

Exon 2 ◽

Tissue Specific ◽

Isolation And Characterization ◽

Carbonic Anhydrase I ◽

Erythroleukemia Cells ◽

Exon 1

We report the isolation and characterization of the mouse carbonic anhydrase I (CAI) gene. Direct RNA sequence analysis of the 5' nontranslated regions of CAI mRNA from mouse colon and mouse erythroleukemia cells demonstrated tissue specificity in the lengths and sequences of CAI transcripts. Analysis of several mouse CAI genomic clones showed that the transcripts arose from a single CAI gene with two tissue-specific promoters and eight exons. CAI transcripts in the colon were found to initiate just upstream of the erythroid exon 2 of the CAI gene region sequence. Erythroid transcripts originated from a novel promoter upstream of exon 1, which was located more than 10 but less than 250 kilobases upstream of exon 2. Erythroid exon 1 contained only a nontranslated sequence, which was spliced to exon 2 via a cryptic splice acceptor site located in the region that encoded the colon mRNA 5' nontranslated sequence. The remaining exon-intron junctions were conserved in comparison with those of the CAII and CAIII genes.

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cDNA Cloning of a Novel Amphiphysin Isoform and Tissue-Specific Expression of Its Multiple Splice Variants

Biochemical and Biophysical Research Communications ◽

10.1006/bbrc.1997.6927 ◽

1997 ◽

Vol 236 (1) ◽

pp. 178-183 ◽

Cited By ~ 49

Author(s):

Ken Tsutsui ◽

Yukihide Maeda ◽

Kimiko Tsutsui ◽

Shuji Seki ◽

Akira Tokunaga

Keyword(s):

Cdna Cloning ◽

Splice Variants ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression

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Tissue-specific expression of splice variants of the mouse voltage-gated calcium channel α2/δ subunit

FEBS Letters ◽

10.1016/s0014-5793(96)01205-7 ◽

1996 ◽

Vol 397 (2-3) ◽

pp. 331-337 ◽

Cited By ~ 45

Author(s):

Timothy Angelotti ◽

Franz Hofmann

Keyword(s):

Calcium Channel ◽

Splice Variants ◽

Specific Expression ◽

Tissue Specific ◽

Voltage Gated ◽

Tissue Specific Expression ◽

Voltage Gated Calcium Channel

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Cloning and identification of tissue-specific expression of KCNN4 splice variants in rat colon

AJP Cell Physiology ◽

10.1152/ajpcell.00091.2009 ◽

2010 ◽

Vol 299 (2) ◽

pp. C251-C263 ◽

Cited By ~ 29

Author(s):

Christian Barmeyer ◽

Christoph Rahner ◽

Youshan Yang ◽

Frederick J. Sigworth ◽

Henry J. Binder ◽

...

Keyword(s):

Amino Acid ◽

Splice Variants ◽

Amino Acid Level ◽

Distal Colon ◽

Rat Colon ◽

Membrane Expression ◽

Specific Expression ◽

Tissue Specific ◽

Anion Secretion ◽

Tissue Specific Expression

KCNN4 channels that provide the driving force for cAMP- and Ca2+-induced anion secretion are present in both apical and basolateral membranes of the mammalian colon. However, only a single KCNN4 has been cloned. This study was initiated to identify whether both apical and basolateral KCNN4 channels are encoded by the same or different isoforms. Reverse transcriptase-PCR (RT-PCR), real-time quantitative-PCR (RT-QPCR), and immunofluorescence studies were used to clone and identify tissue-specific expression of KCNN4 isoforms. Three distinct KCNN4 cDNAs that are designated as KCNN4a, KCNN4b, and KCNN4c encoding 425, 424, and 395 amino acid proteins, respectively, were isolated from the rat colon. KCNN4a differs from KCNN4b at both the nucleotide and the amino acid level with distinct 628 bp at the 3′-untranslated region and an additional glutamine at position 415, respectively. KCNN4c differs from KCNN4b by lacking the second exon that encodes a 29 amino acid motif. KCNN4a and KCNN4b/c are identified as smooth muscle- and epithelial cell-specific transcripts, respectively. KCNN4b and KCNN4c transcripts likely encode basolateral (40 kDa) and apical (37 kDa) membrane proteins in the distal colon, respectively. KCNN4c, which lacks the S2 transmembrane segment, requires coexpression of a large conductance K+ channel β-subunit for plasma membrane expression. The KCNN4 channel blocker TRAM-34 inhibits KCNN4b- and KCNN4c-mediated 86Rb (K+ surrogate) efflux with an apparent inhibitory constant of 0.6 ± 0.1 and 7.8 ± 0.4 μM, respectively. We conclude that apical and basolateral KCNN4 K+ channels that regulate K+ and anion secretion are encoded by distinct isoforms in colonic epithelial cells.

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